FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data

Despite the recent surge of viral metagenomic studies, recovering complete virus/phage genomes from metagenomic data is still extremely difficult and most viral contigs generated from de novo assembly programs are highly fragmented, posing serious challenges to downstream analysis and inference. In this study, we develop FastViromeExplorer (FVE)-novel, a computational pipeline for reconstructing complete or near-complete viral draft genomes from metagenomic data. The FVE-novel deploys FVE to efficiently map metagenomic reads to viral reference genomes, performs de novo assembly of the mapped reads to generate contigs, and extends the contigs through iterative assembly to produce final viral scaffolds. We applied FVE-novel to an ocean metagenomic sample and obtained 268 viral scaffolds that potentially come from novel viruses. Through manual examination and validation of the 10 longest scaffolds, we successfully recovered 4 complete viral genomes, 2 are novel as they cannot be found in the existing databases and the other 2 are related to known phages. This hybrid reference-based and de novo assembly approach used by FVE-novel represents a powerful new approach for uncovering near-complete viral genomes in metagenomic data.